Add a new step to the onboarding workflow reminding AI agents to commit
the `.beads/issues.jsonl` file together with code changes. This ensures
issue state stays synchronized with code state, which is critical for
maintaining accurate project history and making issues meaningful when
reviewing past commits.
- Refactor bd onboard to output instructions instead of doing string replacement
- Leverage agent intelligence to naturally integrate bd into documentation
- Bootstrap via 'BEFORE ANYTHING ELSE: run bd onboard' in AGENTS.md
- Agent receives formatted instructions to update AGENTS.md and CLAUDE.md
- More agentic approach - adapts to existing project structure
- Update README with new bootstrap workflow
Amp-Thread-ID: https://ampcode.com/threads/T-d70fd1bf-8d44-48b6-bb55-5ae49efb23b8
Co-authored-by: Amp <amp@ampcode.com>
